SMTL ID : 7a06.1

Structure of human CKa1 in complex with compound o

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x QTH: 1-[(4-phenylphenyl)methyl]-4-pyrrolidin-1-yl-pyridine(Non-covalent)

QTH.1: 12 residues within 4Å: Chain A: W.174, Y.182, N.231, D.232, Y.259, L.345, W.346, W.349, I.359, F.361, Y.363 Ligands: QTH.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.174, A:L.345, A:W.346, A:W.346, A:W.349, A:W.349, A:I.359, A:F.361, A:F.361 pi-Stacking: A:Y.259 QTH.2: 8 residues within 4Å: Chain A: R.43, Q.234, Y.280, W.346, W.349, F.361, Y.366 Ligands: QTH.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.280, A:Y.280, A:Y.280, A:W.346, A:W.349, A:F.361, A:Y.366 pi-Stacking: A:Y.280 QTH.16: 12 residues within 4Å: Chain B: W.174, Y.182, N.231, D.232, Y.259, L.345, W.346, W.349, I.359, F.361, Y.363 Ligands: QTH.17 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.174, B:L.345, B:W.346, B:W.346, B:W.349, B:W.349, B:I.359, B:F.361, B:F.361 pi-Stacking: B:Y.259 QTH.17: 8 residues within 4Å: Chain B: R.43, Q.234, Y.280, W.346, W.349, F.361, Y.366 Ligands: QTH.16 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.280, B:Y.280, B:Y.280, B:W.346, B:W.349, B:F.361, B:Y.366 pi-Stacking: B:Y.280

26 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: Y.278, A.290, I.292, A.369, D.372, A.373 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: D.6, H.38, I.39, S.40, Q.52, C.53, S.54, K.68 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: R.16, W.20, M.49, L.73, G.75, Q.128 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: E.101, L.105, F.168, N.169 Chain B: F.24, I.125, F.126 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: Y.182, E.185, W.349, V.352, Q.353, I.356 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: R.196, K.199, Y.285, A.354, G.362, Y.363, M.364, D.365 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: M.277, I.292, Y.295, H.343, H.376, Q.377 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: H.38, P.56, D.57, T.58 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: S.320, E.322, E.323 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: K.184, L.187, R.188 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: E.171, P.172, K.173, Y.264 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: F.176, R.216, L.219, E.220, Y.264 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: R.196, Q.353, A.354, S.357, I.359, F.361, Y.363 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: Y.278, A.290, I.292, A.369, D.372, A.373 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain B: D.6, H.38, I.39, S.40, Q.52, C.53, S.54, K.68 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: R.16, W.20, M.49, L.73, G.75, Q.128 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: F.24, I.125, F.126 Chain B: E.101, L.105, F.168, N.169 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: Y.182, E.185, W.349, V.352, Q.353, I.356 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain B: R.196, K.199, Y.285, A.354, G.362, Y.363, M.364, D.365 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: M.277, I.292, Y.295, H.343, H.376, Q.377 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: H.38, P.56, D.57, T.58 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: S.320, E.322, E.323 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: K.184, L.187, R.188 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: E.171, P.172, K.173, Y.264 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: F.176, R.216, L.219, E.220, Y.264 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain B: R.196, Q.353, A.354, S.357, I.359, F.361, Y.363 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Serran-Aguilera, L. et al., Synthesis, biological evaluation, in silico modeling and crystallization of novel small monocationic molecules with potent antiproliferative activity by dual mechanism. Eur.J.Med.Chem. (2020)

Release Date

2020-09-09

Peptides

Choline kinase alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Choline kinase alpha

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